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author davidvanzessen
date Tue, 29 Jan 2019 03:54:09 -0500
parents a24f8c93583a
children 6809c63d9161
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--- a/shm_selection.htm	Thu Dec 07 03:44:38 2017 -0500
+++ b/shm_selection.htm	Tue Jan 29 03:54:09 2019 -0500
@@ -1,128 +1,128 @@
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-
-<p class=MsoNormalCxSpFirst style='text-align:justify'><b><span lang=EN-GB
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>References</span></b></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
-color:black'>Yaari, G. and Uduman, M. and Kleinstein, S. H. (2012). Quantifying
-selection in high-throughput Immunoglobulin sequencing data sets. In<span
-class=apple-converted-space>&nbsp;</span><em>Nucleic Acids Research, 40 (17),
-pp. e134–e134.</em><span class=apple-converted-space><i>&nbsp;</i></span>[</span><span
-lang=EN-GB><a href="http://dx.doi.org/10.1093/nar/gks457" target="_blank"><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
-color:#303030'>doi:10.1093/nar/gks457</span></a></span><span lang=EN-GB
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
-color:black'>][</span><span lang=EN-GB><a
-href="http://dx.doi.org/10.1093/nar/gks457" target="_blank"><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
-color:#303030'>Link</span></a></span><span lang=EN-GB style='font-size:12.0pt;
-line-height:115%;font-family:"Times New Roman","serif";color:black'>]</span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span lang=EN-GB
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Graphs</span></b></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>AA
-mutation frequency</span></u></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>For
-each class, the frequency of replacement mutations at each amino acid position
-is shown, which is calculated by dividing the number of replacement mutations
-at a particular amino acid position/the number sequences that have an amino
-acid at that particular position. Since the length of the CDR1 and CDR2 region
-is not the same for every VH gene, some amino acids positions are absent.
-Therefore we calculate the frequency using the number of amino acids present at
-that that particular location. </span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Antigen
-selection (BASELINe)</span></u></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Shows
-the results of the analysis of antigen selection as performed using BASELINe.
-Details on the analysis performed by BASELINe can be found in Yaari et al,
-PMID: 22641856. The settings used for the analysis are</span><span lang=EN-GB
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>:
-focused, SHM targeting model: human Tri-nucleotide, custom bounderies. The
-custom boundries are dependent on the ‘sequence starts at filter’. </span></p>
-
-<p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL
-style='font-family:UICTFontTextStyleBody;color:black'>Leader:
-1:26:38:55:65:104:-</span></p>
-
-<p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL
-style='font-family:UICTFontTextStyleBody;color:black'>FR1: 27:27:38:55:65:104:-</span></p>
-
-<p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL
-style='font-family:UICTFontTextStyleBody;color:black'>CDR1:&nbsp;27:27:38:55:65:104:-</span></p>
-
-<p class=MsoNormalCxSpLast style='line-height:normal'><span lang=NL
-style='font-family:UICTFontTextStyleBody;color:black'>FR2:&nbsp;27:27:38:55:65:104:-</span></p>
-
-<p class=MsoNormal><span lang=NL style='font-size:12.0pt;line-height:115%;
-font-family:"Times New Roman","serif"'>Hanna IJspeert, Pauline A. van
-Schouwenburg, David van Zessen, Ingrid Pico-Knijnenburg, Gertjan J. Driessen,
-Andrew P. Stubbs, and Mirjam van der Burg (2016). </span><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Evaluation
-of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and
-Adults. In <i>Frontiers in Immunolog, 7, pp. e410-410. </i>[<a
-href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066086/"><span
-style='color:windowtext'>doi:10.3389/fimmu.2016.00410</span></a>][<a
-href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066086/"><span
-style='color:windowtext'>Link</span></a>]</span></p>
-
-</div>
-
-</body>
-
-</html>
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+
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+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
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+
+<div class=WordSection1>
+
+<p class=MsoNormalCxSpFirst style='text-align:justify'><b><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>References</span></b></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
+color:black'>Yaari, G. and Uduman, M. and Kleinstein, S. H. (2012). Quantifying
+selection in high-throughput Immunoglobulin sequencing data sets. In<span
+class=apple-converted-space>&nbsp;</span><em>Nucleic Acids Research, 40 (17),
+pp. e134–e134.</em><span class=apple-converted-space><i>&nbsp;</i></span>[</span><span
+lang=EN-GB><a href="http://dx.doi.org/10.1093/nar/gks457" target="_blank"><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
+color:#303030'>doi:10.1093/nar/gks457</span></a></span><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
+color:black'>][</span><span lang=EN-GB><a
+href="http://dx.doi.org/10.1093/nar/gks457" target="_blank"><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
+color:#303030'>Link</span></a></span><span lang=EN-GB style='font-size:12.0pt;
+line-height:115%;font-family:"Times New Roman","serif";color:black'>]</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Graphs</span></b></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>AA
+mutation frequency</span></u></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>For
+each class, the frequency of replacement mutations at each amino acid position
+is shown, which is calculated by dividing the number of replacement mutations
+at a particular amino acid position/the number sequences that have an amino
+acid at that particular position. Since the length of the CDR1 and CDR2 region
+is not the same for every VH gene, some amino acids positions are absent.
+Therefore we calculate the frequency using the number of amino acids present at
+that that particular location. </span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Antigen
+selection (BASELINe)</span></u></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Shows
+the results of the analysis of antigen selection as performed using BASELINe.
+Details on the analysis performed by BASELINe can be found in Yaari et al,
+PMID: 22641856. The settings used for the analysis are</span><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>:
+focused, SHM targeting model: human Tri-nucleotide, custom bounderies. The
+custom boundries are dependent on the ‘sequence starts at filter’. </span></p>
+
+<p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL
+style='font-family:UICTFontTextStyleBody;color:black'>Leader:
+1:26:38:55:65:104:-</span></p>
+
+<p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL
+style='font-family:UICTFontTextStyleBody;color:black'>FR1: 27:27:38:55:65:104:-</span></p>
+
+<p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL
+style='font-family:UICTFontTextStyleBody;color:black'>CDR1:&nbsp;27:27:38:55:65:104:-</span></p>
+
+<p class=MsoNormalCxSpLast style='line-height:normal'><span lang=NL
+style='font-family:UICTFontTextStyleBody;color:black'>FR2:&nbsp;27:27:38:55:65:104:-</span></p>
+
+<p class=MsoNormal><span lang=NL style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'>Hanna IJspeert, Pauline A. van
+Schouwenburg, David van Zessen, Ingrid Pico-Knijnenburg, Gertjan J. Driessen,
+Andrew P. Stubbs, and Mirjam van der Burg (2016). </span><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Evaluation
+of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and
+Adults. In <i>Frontiers in Immunolog, 7, pp. e410-410. </i>[<a
+href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066086/"><span
+style='color:windowtext'>doi:10.3389/fimmu.2016.00410</span></a>][<a
+href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066086/"><span
+style='color:windowtext'>Link</span></a>]</span></p>
+
+</div>
+
+</body>
+
+</html>